R/4.2.1: missing packages?

It seems that the latest R/4.2.1 version is missing some packages, although they are mentioned in the announce post New software installed R 4.2.1 ?

Take for example tidyverse and sf, both are on the list but not installed? It seems it is an omission, as tidyverse was there for almost all versions (check find /opt/ebsofts/R -type d -name "*tidyverse*" -print).

Also, when running module spider R/4.2.1, zero Included extensions are listed, unlike previous versions (and unlike in the post?)

Minimum reproducible code

module load GCC/11.3.0  OpenMPI/4.1.4 R/4.2.1
pkgs_here <- installed.packages(lib.loc="/opt/ebsofts/R/4.2.1-foss-2022a/lib64/R/library")[,"Package"]
any(pkgs_here %in% c("tidyverse", "sf"))

will return FALSE whereas it should be TRUE

Just following-up on this, besides missing packages (tidyverse, sf), it seems there are also packages that were not well installed?

See the empty folder for package terra (ls /opt/ebsofts/R/4.2.1-foss-2022a/lib64/R/library/terra), which is not empty for other versions (check ls /opt/ebsofts/R/4.2.0-foss-2021b/lib64/R/library/terra for example).

The problem seems to be the same on yggdrasil, with the same issues (missing packages, weird terra folder), presumably installed with the same problematic script?

Hi Matthieu,

I just installed the latest version of R, could you try it and let me know if it’s working well ?

Oh nice, great to hear about the new installation!

Unfortunately, it looks like the problem was “solved” by offering much less extensions than before? I count up to 1000 packages installed with 4.2.0, but only ~110 with 4.3.3?

Ideally, do you think you could maintain consistency with the same packages pre-compiled across R versions? If not, would it be possible to include at least the package tidyverse with R 4.3.3? It has become the most popular R package, so is likely so be useful to many users here!?


For a rough count of packages:

find /opt/ebsofts/R/4.3.3-*/lib64/R/library/* -maxdepth 0 -type d | wc -l
find /opt/ebsofts/R/4.2.0-*/lib64/R/library/* -maxdepth 0 -type d | wc -l

Also, note that R 4.3.3 is not the latest, as in the meanwhile 4.4.0 and 4.4.1 came out (ok, the latter very recently, on June 14) :wink: